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Peer-reviewedCC BY 4.0G3: Genes, Genomes, Genetics

The chromosome-level annotated reference genome MakAnk1.0 reveals a putative signature of selection for long horns and provides insights into the demographic history of Ankole cattle

  • Rodney Okwasiimire1,2
  • Kisun Pokharel2
  • Melak Weldenegodguad3
  • Mahlako L Makgahlela4,5
  • Nasser Ghanem6
  • Catarina Ginja7,8
  • Junxin Gao9
  • Pekka Uimari1
  • Juha Kantanen2
  • Donald R Kugonza10
  • Richard P M A Crooijmans9
10 affiliations
  1. 1Department of Agricultural Sciences, University of Helsinki , 00014 Helsinki ,
  2. 2Natural Resources Institute Finland , 31600 Jokioinen ,
  3. 3Natural Resources Institute Finland , 00790 Helsinki ,
  4. 4Animal Breeding and Genetics, Agricultural Research Council , Irene 0062, Pretoria ,
  5. 5Department of Animal Science, University of the Free State , 9301 Bloemfontein ,
  6. 6Department of Animal Production, Faculty of Agriculture, Cairo University , Giza 12613, Cairo ,
  7. 7CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto , 4485-661 Vairão ,
  8. 8BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO , 4485-661 Vairão ,
  9. 9Animal Breeding and Genomics, Wageningen University and Research , 6708 PB Wageningen ,
  10. 10Department of Animal and Range Sciences, College of Agricultural and Environmental Sciences, Makerere University , P.O. Box 7062, Kampala ,
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Abstract

Long-horned Ankole cattle belong to the Sanga group of cattle, which is widely distributed throughout sub-Saharan Africa. They are valued for disease, vector, and parasite tolerance, adaptation to harsh tropical environments, in addition to their unique cultural significance. In this study, a haplotype-aware, chromosome-resolved genome of Ankole cattle (MakAnk1.0) spanning 2.84 Gb, with a scaffold N50 of 110.9 Mb was assembled from PacBio HiFi and Omni-C data. The primary assembly attained 99.5% BUSCO completeness, while haplotypes 1 and 2 had lengths of 2.69 and 2.62 Gb, scaffold N50 of 106.41 and 106.48 Mb, and BUSCO scores of 98.9% and 96.7%, respectively. Gene prediction for the primary assembly yielded 19,406 genes, with a BUSCO completeness score of 88.7%. Repeat sequences accounted for 56.41% of the primary assembly, whereas haplotypes 1 and 2 contained 54.71% and 54.86%, respectively. Using the assembled genome, 27.5 million SNPs and 3.6 million INDELs were discovered, while genome-wide RAiSD analysis identified 421 candidate genomic regions under selection, from which 256 genes were subsequently annotated. These included the HLCS gene, which plays a role in biotinylation and keratinization, potentially supporting development of the long horns in Ankole cattle. Moreover, the annotated genes under selection overlapped with economically significant QTLs in tropical cattle, including tick resistance. Furthermore, the estimated recent effective population size (Ne) trajectory revealed a population contraction, with contemporary Ne estimates ranging from 228 to 278. Collectively, this study provides a valuable genomic resource for advancing research, breed improvement, and conservation of the transboundary Ankole cattle.

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Cite

BibTeXRIS
BibTeX
@article{okwasiimire2026chromosomelevel,
  title = {{The chromosome-level annotated reference genome MakAnk1.0 reveals a putative signature of selection for long horns and provides insights into the demographic history of Ankole cattle}},
  author = {Rodney Okwasiimire and Kisun Pokharel and Melak Weldenegodguad and Mahlako L Makgahlela and Nasser Ghanem and Catarina Ginja and Junxin Gao and Pekka Uimari and Juha Kantanen and Donald R Kugonza and Richard P M A Crooijmans},
  journal = {G3: Genes, Genomes, Genetics},
  year = {2026},
  month = oct,
  doi = {10.1093/g3journal/jkag287},
  url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag287/9002841},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - The chromosome-level annotated reference genome MakAnk1.0 reveals a putative signature of selection for long horns and provides insights into the demographic history of Ankole cattle
AU  - Rodney Okwasiimire
AU  - Kisun Pokharel
AU  - Melak Weldenegodguad
AU  - Mahlako L Makgahlela
AU  - Nasser Ghanem
AU  - Catarina Ginja
AU  - Junxin Gao
AU  - Pekka Uimari
AU  - Juha Kantanen
AU  - Donald R Kugonza
AU  - Richard P M A Crooijmans
PY  - 2026
DA  - 2026/10/27
JO  - G3: Genes, Genomes, Genetics
DO  - 10.1093/g3journal/jkag287
UR  - https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag287/9002841
AB  - Long-horned Ankole cattle belong to the Sanga group of cattle, which is widely distributed throughout sub-Saharan Africa. They are valued for disease, vector, and parasite tolerance, adaptation to harsh tropical environments, in addition to their unique cultural significance. In this study, a haplotype-aware, chromosome-resolved genome of Ankole cattle (MakAnk1.0) spanning 2.84 Gb, with a scaffold N50 of 110.9 Mb was assembled from PacBio HiFi and Omni-C data. The primary assembly attained 99.5% BUSCO completeness, while haplotypes 1 and 2 had lengths of 2.69 and 2.62 Gb, scaffold N50 of 106.41 and 106.48 Mb, and BUSCO scores of 98.9% and 96.7%, respectively. Gene prediction for the primary assembly yielded 19,406 genes, with a BUSCO completeness score of 88.7%. Repeat sequences accounted for 56.41% of the primary assembly, whereas haplotypes 1 and 2 contained 54.71% and 54.86%, respectively. Using the assembled genome, 27.5 million SNPs and 3.6 million INDELs were discovered, while genome-wide RAiSD analysis identified 421 candidate genomic regions under selection, from which 256 genes were subsequently annotated. These included the HLCS gene, which plays a role in biotinylation and keratinization, potentially supporting development of the long horns in Ankole cattle. Moreover, the annotated genes under selection overlapped with economically significant QTLs in tropical cattle, including tick resistance. Furthermore, the estimated recent effective population size (Ne) trajectory revealed a population contraction, with contemporary Ne estimates ranging from 228 to 278. Collectively, this study provides a valuable genomic resource for advancing research, breed improvement, and conservation of the transboundary Ankole cattle.
SN  - 2160-1836
ER  -